Is FLNC p.Thr599= (c.1797C>T) pathogenic?

FLNC p.Thr599= (c.1797C>T) is classified Likely benign in FLNC (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-06-01). Very rare (popmax 0.00454%, eas); Associated with Cardiovascular phenotype.

What condition is associated with FLNC p.Thr599= (c.1797C>T)?

FLNC p.Thr599= (c.1797C>T) is associated with Cardiovascular phenotype, cardiomyopathy, myofibrillar myopathy 5 (ClinVar).

How common is FLNC p.Thr599= (c.1797C>T) in the general population?

FLNC p.Thr599= (c.1797C>T) is very rare (popmax 0.00454%, eas) (gnomAD).

FLNC p.Thr599=

c.1797C>T · rs773793586 · VCV384275

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00454%, eas)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.6
Overall
CADD	4.744	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00454% East Asian · 2/44,094 alleles

Filtering AF 0.00146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00124%

Overall 0.00181% 29/1,598,736 alleles · very rare exomes 27/1,447,204 · genomes 2/151,532 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00454%	22,047
South Asian	0.00223%	44,747
European (non-Finnish)	0.00213%	46,908

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: FLNC
Protein: p.Thr599=
Coding: c.1797C>T
MANE Select: NM_001458
dbSNP: rs773793586
Type: single nucleotide variant
Location: chr7:128840954 (GRCh38)
Gene constraint: LOEUF 0.424 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 599: a β-strand

Full FLNC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy myofibrillar myopathy 5 distal myopathy with posterior leg and anterior hand involvement hypertrophic cardiomyopathy 26

Similar variants

FLNC c.1047+1G>T Likely pathogenic ★★ same condition
FLNC c.1048-1G>A Likely pathogenic ★★ same condition
FLNC c.1210+1G>A Likely pathogenic ★★ same condition
FLNC c.1549+2T>G Likely pathogenic ★★ same condition
FLNC c.2007+1G>A Likely pathogenic ★★ same condition
FLNC c.2550+1G>C Likely pathogenic ★★ same condition
FLNC c.2550+2T>C Pathogenic/Likely pathogenic ★★ same condition
FLNC c.2930-1G>A Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/flnc-p-thr599 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown